Direct evidence‐based approaches are vital in understanding the involvement of abiotic/biotic factors and evaluating the newly proposed theories on soil carbon (C) stabilization. Microaggregates (150–250 µm) collected from a corn system (>22 years; Kansas, USA), which had been under no‐till with different nitrogen (N) treatments were analyzed (N treatments: manure/compost, urea, zero fertilizer). We studied C stabilization in free soil microaggregates (with preserved aggregate architecture), directly using scanning transmission X‐ray microscopy coupled with near edge X‐ray absorption fine structure (STXM‐NEXAFS) spectroscopy. Submicron scale findings were complemented with bulk chemical analysis. The STXM‐NEXAFS analysis revealed soil organic carbon (SOC) preservation inside nano‐ and micro‐pores and organo–mineral association, various degrees of humification, and high molecular diversity. The presence of microbial‐derived C was found in manure‐/compost‐added microaggregates highlighting the contribution of organic amendments in facilitating microbial diversity. The incidence of aragonite‐like minerals suggested the biologically/chemically active nature of microaggregate cores. Bulk analysis of free microaggregates showed a higher concentration of SOC (6.5%), ammonium oxalate extractable Fe/Al/Si), and higher aliphaticity of humic acid in manure‐/compost‐added soils compared to inorganic fertilizer (3% SOC) and control (2.7% SOC) treatments. The co‐existence of elements (calcium [Ca]/C, iron [Fe]/N, Fe/C, aluminum [Al]/C, and silicon [Si]/C) was partially supported by bulk chemical analysis that indicated a strong association between ammonium oxalate extractable Fe/Al/Si and SOC (R2 = 0.63—0.77). Overall, our study provided direct/indirect evidence for the complex and interactive involvement of chemical, mineralogical, and biological mechanisms that may have been stimulated by the long‐term addition of compost/manure in stabilizing SOC.